RNA-seq, like our other services, has no single fixed price. The cost depends primarily on the number of samples, library type, amount of data per sample and the scope of the service.
Standard mRNA-seq with Poly(A) selectionis usually the most economical option. Total RNA-seq, low-input RNA-seq and full-length transcript analysis require more advanced protocols and more expensive library preparation kits, and are usually more expensive.
What affects the price of RNA-seq?
| Project component | Effect on price |
|---|---|
| Number of samples | More samples usually mean a lower price per sample |
| RNA isolation | Additional cost if biological material is supplied |
| Quality control | Includes measurements of RNA quantity, purity and integrity - included in the service price |
| Library type | Poly(A), stranded, rRNA depletion, small RNA and low-input workflows require different library preparation kits and vary in price |
| Amount of data | A higher number of reads increases the sequencing cost |
| Sequencing mode | Paired-end sequencing is usually more expensive than single-end sequencing |
| Bioinformatics analysis | Cost depends on the scope and number of comparisons |
| Material quality | Poor-quality samples may require additional preparation, namely clean-up, which may incur additional costs. |
| Data delivery | Projects generating more than 800 Gb of data require the results to be sent by courier on an external drive |
RNA-seq type and cost
mRNA-seq with Poly(A) selection
The most commonly chosen and usually the most economical option for eukaryotic organisms. It is primarily used to analyse the expression of protein-coding genes.
The standard workflow usually includes:
- a stranded library,
- paired-end sequencing at 2 × 150 bp,
- a recommended data output of approximately 6-10 Gb per sample,
- gene expression and DEG analysis.
Total RNA-seq with rRNA depletion
It is usually more expensive than mRNA-seq because:
- library preparation requires rRNA removal,
- more transcript classes are analysed,
- a larger amount of data is required,
- bioinformatics analysis is more extensive.
The recommended data output is approximately 12-16 Gb per sample.
Low-input RNA-seq
The cost depends on the number of cells or the amount of RNA, as well as the selected protocol. If the material quantity is low, specialised kits, more amplification cycles and different quality control procedures may be required.
small RNA-seq
It requires a separate approach to library preparation, size selection of short fragments and dedicated bioinformatics analysis. It is not a standard add-on to mRNA-seq or Total RNA-seq.
Full-length transcriptome
Full-length transcript sequencing on a PacBio or Oxford Nanopore platform is usually more expensive than conventional Illumina RNA-seq. It is used when the aim is to analyse complete isoforms and alternative splicing.
How does the amount of data affect the price?
The greater the amount of data per sample, the higher the sequencing cost.
| Option | Approximate data output | Typical application |
|---|---|---|
| Basic mRNA-seq | 6 Gb | Standard DEG analysis |
| Extended mRNA-seq | 10 Gb | Genes expressed at lower levels |
| Deep mRNA-seq | 15 Gb | Splicing, isoforms, novel transcripts |
| total RNA-seq | 12 Gb | mRNA and lncRNA |
| Extended Total RNA-seq | 16 Gb | Analysis including circRNA |
Choosing the highest data output is not always worthwhile. For standard DEG analysis, increasing the number of biological replicates may be more beneficial than sequencing a small number of samples at very high depth.
How does the number of samples affect the price?
The cost per sample usually decreases as the number of samples increases, because library preparation kits and available sequencer throughput can be used more efficiently.
Small projects may be relatively more expensive per sample because of:
- the minimum laboratory batch size,
- the cost of library preparation,
- the need to wait for a library pool,
- fixed analysis and reporting costs.
You should not reduce the number of biological replicates solely to lower the price. A statistically underpowered study may fail to provide reliable results.
What can increase the project cost?
- RNA isolation from tissues or cells,
- low-input or FACS-sorted samples,
- FFPE or degraded material,
- the need for a non-standard library preparation kit,
- greater sequencing depth,
- repeat library preparation from a sample that does not meet the requirements.
Sample Requirements
For standard mRNA-seq, the following is recommended:
- more than 0.5 µg of total RNA,
- a concentration above 50 ng/µl,
- a volume above 20 µl,
- OD260/280: 1.8-2.2,
- RIN above 7, or above 6 for plants.
Providing RNA that meets the requirements reduces the risk of additional costs and delays. Low-input, FFPE or lower-quality samples require a case-by-case assessment.
Common mistakes when comparing quotations
- comparing only the price per sample,
- not accounting for the number of reads or Gb per sample,
- confusing individual reads with read pairs,
- a lack of information on whether the price includes library preparation,
- a lack of information on bioinformatics analysis,
- comparing mRNA-seq with Total RNA-seq,
- not accounting for RNA isolation,
- choosing too few biological replicates,
- ordering more data than the project objective requires,
- not checking whether the quoted price excludes or includes VAT.
Questions for a project quotation
Have answers to the following questions ready so we can prepare an accurate quotation:
Get a quotation
Describe your project - we will recommend a method and amount of data.
Based on the number of samples, material quality and study objective, we will prepare a tailored quotation covering RNA isolation, quality control, library preparation, sequencing and the selected scope of bioinformatics analysis.
Selected projects and client publications
See which institutions we perform next-generation sequencing (NGS) for and explore scientific publications that draw on the data we have supplied.